SUMMARY Early-life changes in the respiratory microbiome appear to have a substantial impact on the risk of developing respiratory morbidity, including infant infections and recurrent wheezing illnesses. There are currently no primary preventive strategies for these disorders. Acute respiratory illnesses (ARIs) during infancy, particularly with Respiratory Syncytial Virus (RSV) are a well-known risk factor for childhood asthma. Our preliminary data suggests that presence of Lactobacillus and Staphylococcus in nasopharynx during acute RSV infection is associated to be protective for the year 2 wheezing outcomes, although the mechanisms behind these associations remain largely unknown. Understanding these relationships could lead to the development of primary prevention strategies for the development of childhood asthma. Our hypothesis is that specific function(s) of URT microbiome community, and their interactions modulate host immune responses during and following RSV ARI, subsequently protecting against development of recurrent wheeze and childhood asthma. To address our hypotheses, in Aim 1, we plan to use metagenomic sequencing to characterize URT microbiome community at species level in existing nasal wash samples from a birth cohort in which first infant RSV infection is captured, and recurrent wheezing illnesses are assessed annually. In Aim 2, we will perform metatranscriptomic analysis to understand mechanism of Lactobacillus and other URT microbiome (e.g., Staphylococcus) mediated protection of RSV mediated wheezing through transcriptome- based analysis of molecular pathways. The proposed investigation will be the first study to use metagenomic and metatranscriptomic sequencing to describe the early-life microbiome (during RSV infection) and to study its interactions with the development of childhood asthma. Results from this project could lead to the future development of primary prevention strategies to reduce acute infant respiratory morbidity and subsequent childhood asthma. Further, this study will establish a strong basis for clinical trials to use specific bacteria species (e.g., Lactobacillus spp. or a combination of Lactobacillus spp.) as an immunobiotic intervention to ameliorate RSV mediated early-life acute and chronic respiratory outcomes.